Detection of Peptide-Binding Sites on Protein Surfaces Using the Peptimap Server
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Peptide-mediated interactions are of primordial importance to the cell, and the structure of such interaction provides an important starting point for their further characterization. In many cases, the structure of the peptide-protein complex has not been solved by experiment, and modeling tools need to be applied to generate structural models of the interaction. PeptiMap is a protocol that identifies the peptide-binding site when only the structure of the receptor is known, but no information about where the peptide binds is available. This is achieved by mapping the surface for solvents to identify ligand-binding sites, similar in approach to ANCHORMAP in which amino acids are mapped. Peptimap is a free open access web-based server. It can be accessed at http://peptimap.cluspro.org.
Key wordsPeptide-protein interactions Binding site prediction Solvent mapping Peptide mapping
- 14.Lavi A, Ngan CH, Movshovitz-Attias D, Bohnuud T, Yueh C, Beglov D, Schueler-Furman O, Kozakov D (2013) Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions. Proteins 81:2096–2105CrossRefPubMedPubMedCentralGoogle Scholar
- 19.Tomoo K, Matsushita Y, Fujisaki H, Abiko F, Shen X, Taniguchi T, Miyagawa H, Kitamura K, Miura K, Ishida T (2005) Structural basis for mRNA Cap-Binding regulation of eukaryotic initiation factor 4E by 4E-binding protein, studied by spectroscopic, X-ray crystal structural, and molecular dynamics simulation methods. Biochim Biophys Acta 1753:191–208CrossRefPubMedGoogle Scholar
- 21.Brooks BR III, Jr CLB, Nilsson ADM, Petrella L, Roux RJ, Won B, Archontis Y, Bartels G, Boresch C, Caflisch S, Caves A, Cui L, Dinner Q, Feig AR, Fischer M, Gao S, Hodoscek J, Im M, Kuczera W, Lazaridis K, Ma T, Ovchinnikov J, Paci V, Pastor E, Post RW, Pu CB, Schaefer JZ, Tidor M, Venable B, Woodcock RM, Wu HL, Yang X, York WDM, Karplus M (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545–1614CrossRefPubMedPubMedCentralGoogle Scholar